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- PDB-6k6j: The crystal structure of light-driven cyanobacterial chloride imp... -

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Basic information

Entry
Database: PDB / ID: 6k6j
TitleThe crystal structure of light-driven cyanobacterial chloride importer from Mastigocladopsis repens with Bromide ion
ComponentsCyanobacterial chloride importer
KeywordsMEMBRANE PROTEIN / chloride ion pump / rhodopsin
Function / homologyRhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha / BROMIDE ION / OLEIC ACID / RETINAL
Function and homology information
Biological speciesMastigocladopsis repens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYun, J.H. / Park, J.H. / Jin, Z. / Ohki, M. / Wang, Y. / Lupala, C.S. / Kim, M. / Liu, H. / Park, S.Y. / Lee, W.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)20171A2B2008483 Korea, Republic Of
National Research Foundation (Korea)20161A6A3A04010213 Korea, Republic Of
CitationJournal: To Be Published
Title: The crystal structure of light-driven cyanobacterial chloride importer from Mastigocladopsis repens with Bromide ion
Authors: Yun, J.H. / Park, J.H. / Jin, Z. / Ohki, M. / Wang, Y. / Lupala, C.S. / Kim, M. / Liu, H. / Park, S.Y. / Lee, W.
History
DepositionJun 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanobacterial chloride importer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,45918
Polymers26,0611
Non-polymers4,39917
Water1448
1
A: Cyanobacterial chloride importer
hetero molecules

A: Cyanobacterial chloride importer
hetero molecules

A: Cyanobacterial chloride importer
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, The buried subunit interface area was analyzed using the PISA interface. Additionally, analytical size exclusion gel chromatography (aSEC) was also used to confirm that the ...Evidence: gel filtration, The buried subunit interface area was analyzed using the PISA interface. Additionally, analytical size exclusion gel chromatography (aSEC) was also used to confirm that the trimeric form was the only species found in solution.
  • 91.4 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)91,37854
Polymers78,1823
Non-polymers13,19651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area21170 Å2
ΔGint-48 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.618, 61.618, 240.176
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Cyanobacterial chloride importer


Mass: 26060.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mastigocladopsis repens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.9 / Details: Magnesium nitrate hexahydrate, Sodium citrate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→29.8 Å / Num. obs: 8644 / % possible obs: 85 % / Redundancy: 4.6 % / Biso Wilson estimate: 27.05 Å2 / Net I/σ(I): 10.6
Reflection shellResolution: 2.5→2.56 Å / Num. unique obs: 517

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MxDCdata collection
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ITC

5itc


Resolution: 2.5→29.8 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.839 / SU R Cruickshank DPI: 0.78 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 1.183 / SU Rfree Blow DPI: 0.337 / SU Rfree Cruickshank DPI: 0.333
RfactorNum. reflection% reflectionSelection details
Rfree0.267 410 4.74 %RANDOM
Rwork0.194 ---
obs0.197 8642 85.4 %-
Displacement parametersBiso mean: 29.74 Å2
Baniso -1Baniso -2Baniso -3
1-6.2744 Å20 Å20 Å2
2--6.2744 Å20 Å2
3----12.5488 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.5→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 207 8 1952
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011983HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12643HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d713SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes303HARMONIC5
X-RAY DIFFRACTIONt_it1983HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion18.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion236SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2353SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2954 -4.85 %
Rwork0.2116 412 -
all0.2159 433 -
obs--78.43 %

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